2005 Publications

Bahar, Ivet & Rader, AJ. (2005) Tobi, Dror & Bahar, Ivet. (2005) Structural Changes Involved in Protein Binding Correlate with intrinsic Motions of Proteins in the Unbound State. Proc Natl Acad Sci (USA) 102, 18908-18913. [JIF: 9.643]
Berberich, Jason, Yang, Lee Wei, Bahar, Ivet & Russell, Alan J (2005) Analysis of the impact of silver ions on creatine amidinohydrolase. ACTA Biomaterialia 1(2) pg.183-191. [JIF: 2.132]
Berberich, Jason, Yang, Lee Wei, Madura, Jeff, Bahar, Ivet & Russell, Alan J. (2005) A Stable Three Enzyme Creatinine Biosensor Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase. ACTA Biomaterialia 1(2) pg.173-181. [JIF: 2.132]
Chennubhotla, Chakra, Rader, AJ, Yang, Lee-Wei & Bahar, Ivet. (2005) Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies Physical Biology 2, S173-S180. [JIF: 2.773]
Rader, AJ, Vlad, Daniel & Bahar, Ivet (2005) Maturation Dynamics of Bacteriophage HK97 Capsid Structure (Camb) 13:413-21. [JIF: 5.738]
Ramaswamy, Amutha, Bahar, Ivet & Ioshikhes, Ilya (2005) Structural Dynamics of Nucleosome Core Particle: Comparison with Nucleosomes Containing Histone Variants Proteins: Structure, Function and Bioinformatics 58:683-696. [JIF: 3.73]
Yang, Lee Wei & Bahar, Ivet. (2005) Coupling between Catalytic Site and Collective Dynamics: A requirement for Mechanochemical Activity of Enzymes. Structure 13: 893-904. [JIF: 5.738]
Yang, Lee Wei, Liu, Xiong, Jursa, Christopher Jon, Holliman, Mark, Rader, A.J., Karimi, Hassan & Bahar, Ivet. (2005) iGNM: A Database of Protein Functional Motions Based on Gaussian Network Model. Bioinformatics 21: 2978 – 2987. [JIF: 4.894]
Alexander, A.M., Pecoraro, C., Styche, A., Rudert, W.A., Benos, P.V., Ringquist, S., Trucco, M. (2005) SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing, Biotechniques38:87-94. [JIF: 2.462]
Corcoran, D.L., Feingold, E., Dominick, J., Wright, M., Harnaha, J., Trucco, M., Giannoukakis, N., Benos, P.V. (2005) FOOTER: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements, Genome Res.15:840-847. [JIF: 10.256]
Corcoran, D.L., Feingold, E., Benos, P.V. (2005) FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Nucl Acids Res. (2005) 33:W442-446. [JIF: 6.317]
Mahony, S., Golden, A., Smith, T.J., Benos, P.V. (2005) Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. Intelligent Systems in Molecular Biology, Bioinformatics, 21 (Suppl 1):i283-i291. (Approval conference publication rate for ISMB: 13%) [JIF: 4.894]
Ringquist, S., Pecoraro, C., Gilchrist, C., Styche, A., Rudert, W., Benos, P.V. , Trucco, M. (2005) SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms. Nucl Acids Res.33:W548-552. [JIF: 6.317]
Rogulski, K.R., Cohen, D.E., Corcoran, D.L., Benos, P.V. , Prochownik, E.V. (2005) Deregulation of common genes by c-Myc and its direct target, MT-MC1. Proc Natl Acad Sci USA 102:18968-18973. [JIF: 9.643]
Workman, C.T., Yin, Y., Corcoran, D.L., Ideker, T., Stormo, G.D., Benos, P.V. enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucl Acids Res.33:W389-392. [JIF: 6.317]
Camacho CJ. (2005) Modeling side chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins. 2005 60, 245-251. [JIF: 3.73]
Camacho CJ, Zhang C (2005) FastContact: rapid estimate of contact and binding free energies Bioinformatics 2005; 21: 2534-2536. [JIF: 4.894]
Comeau SR, Camacho CJ (2005) Predicting oligomeric assemblies: N-mers a primer. J. Struct. Biol. 2005; 150: 233-244. [JIF: 3.496]
Comeau S, Vajda S, Camacho CJ. (2005) Performance of the first protein docking server ClusPro in CAPRI rounds3-5. Proteins. 2005 60, 239-244. [JIF: 3.73]
Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. (2005) Optimal clustering for detecting near native conformations in protein docking. Biophys. J. 2005 89, 867-875. [JIF: 4.757]
Chen, P. Y., Manninga, H., Slanchev, K., Chien, M., Russo, J. J., Ju, J., Sheridan, R., John, B., Marks, D. S., Gaidatzis, D., Sander, C., Zavolan, M. & Tuschl, T. (2005). The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 19, 1288-93. [JIF: 15.05]
Topf, M., Baker, M. L., John, B., Chiu, W. & Sali, A. (2005). Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol 149, 191-203. [JIF: 3.496]
Cheluvaraja S, Meirovitch H. (2005) Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo Method: Application to peptides. J. Chem. Phys. 2005:122, 054903-1 - 054903-14. 10904. [JIF: 3.166]
Cheluvaraja S, Meirovitch H. (2005) Calculation of the entropy and free energy from Monte Carlo simulations of a peptide stretched by an external force. J. Phys. Chem. B. 109, 21963-21970. [JIF: 4.115]
White RP, Funt J, Meirovitch H. (2005) Calculation of the entropy of lattice polymer models from Monte Carlo trajectories. Chem. Phys. Lett. 410, 430-435. [JIF: 2.462]
White RP, Meirovitch H. (2005) Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo Method. J. Chem. Phys. 123, 214908-11. [JIF: 3.166] Ytreberg, F. M. and Zuckerman, D. M. (2005) Peptide Conformational equilibria computed via a single-stage shifting protocol, J. Phys. Chem. B., 109:9096-9103. [JIF: 4.115]

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2005 Publications